Have you read the reports of other travelers? (Including Japanese domestic riders one)
Japan is long fr north(Hokkaido) to south(Okinawa), there are regional differences in temperature and humidity.
It is thought that Japan is a very small island country bc it is located in the east end in the world map,
(the one of Asia's absence in the West)
but in fact it is Not.(Do you know this web?)
http://thetruesize.com/Basic climate of regions is explained by JMA,wiki and more.
http://www.data.jma.go.jp/gmd/cpd/longfcst/en/tourist.htmlhttp://www.data.jma.go.jp/gmd/cpd/longfcst/en/tourist_japan.htmlhttps://en.wikipedia.org/wiki/Geography_of_Japan#ClimateIf you want to run even in the rainy season,
it is better to go up fr warmer south to north before rainy season
and goal at Hokkaido during the rainy season also CTS out easier.
There are about 10 regions in Japan from Hokkaido to Okinawa Prefecture,
but in here will explain them in 4 of part.
http://wikitravel.org/en/JapanHokkaido :
Fr early summer to early autumn, No rainy season and lower humidity very comfort.
Although there are more nature than other areas,
it can be said that it is easy to become somewhat monotonous scenery.
Hokkaido is really really wide, see the map :)
Main land(Honshu) :
Spring till the rainy season and fall. Higher mountains area in summer also good.
Japanese riders will also concentrate on summer due to calendar relationship.
Shikoku, Kyushu and Okinawa :
Mild and no snowfall, you can run in winter. (except for some areas)
But it is easy to become a passage of typhoon fr the early summer to fall,
if you hit directly, 3 days will be stuck, and summer is pretty hot
so do not recommend if no experiences hot and humid countries than Japan.
This Japanese rider has just traversed about 3000km in 25 days total fr north to south in 1990.
but he has not dropped in many areas such as famous big city Tokyo.
http://www.geocities.jp/flyfishing_lover/travel-index.html(He living in Tokyo)
This is mid 60ty rider challenged longer about 5500km in 47 days total.
http://yasudafamily.sakura.ne.jp/hitori/judan.htmlThis is rickshaw challenged about 6000km. (red lines : ferry)
https://cdn.camp-fire.jp/jbimages/68f7a07a-b70f-41d4-b27f-4cf749bb9369...The distance can be examined by Google map, but can not calculate by bicycle.
Please search by foot or car(as excluding toll road).
Depending on type of bicycle and height difference, it would be safer to keep it around 100km/day.
Be careful as bicycle shops will be few if you leave the urban area.
The risk of punk is lower than any country, but it may still be experienced once in a long distance ride.
If you take a train with bicycle, you need a carry bag, except for some regional railways.
http://blog.worldcycle.co.jp/20140623/11129/Basically there are no cycle racks that are common in Europe.